Jeb Magruder, a former high-level aide to President Richard M. Nixon who went to jail in the Watergate affair and who years later made the startling assertion that Nixon himself had ordered the break-in that set the scandal in motion, died Sunday in Danbury, Connecticut. He was 79.

His death, announced Friday, was caused by complications after a stroke, his family said.

Released from prison in 1975 after seven months, Magruder, a former successful businessman, went on to earn a master’s degree from Princeton Theological Seminary and serve as a Presbyterian pastor. For years he preferred not to speak about the scandal that led to Nixon’s downfall.

But he eventually yielded to continued questions about it, acknowledging in interviews that Nixon had not just covered up the burglary — at the Democratic Party’s national headquarters in the Watergate complex in Washington — but had been involved from the start.

To most Americans, Magruder was a little-known White House communications adviser and the deputy director of Nixon’s re-election campaign when, in January 1973, his name came up during the trial of five men accused of burglarizing the Democratic offices. Their intent, prosecutors said, was to bug the phone of Lawrence F. O’Brien Jr., the party chairman.

Two other White House aides, G. Gordon Liddy and E. Howard Hunt, were also being tried, as conspirators, accused of organizing the break-in.

Hugh W. Sloan Jr., who had been the campaign treasurer, testified in federal court that Magruder had told him to disburse $199,000 to Liddy for “intelligence gathering.”

In later testimony, Magruder denied giving the burglars any assignment concerning the Democratic headquarters. When that was shown to be a lie, he was convicted of perjury and given a 10-month to four-year prison term.

The suggestion that a top campaign official had directly ordered the break-in gave momentum to the investigations in Congress that would finally prompt Nixon to resign Aug. 9, 1974. In return for a lighter sentence, Magruder helped the investigations into others who had been involved.

But not until 2003, in interviews with PBS and The Associated Press, did Magruder drop his bombshell: that he had heard Nixon personally authorize the break-in.

Magruder recalled that on March 30, 1972, in Key Biscayne, Florida, he raised the possibility of bugging O’Brien’s phone — an idea that had already been discussed — in a conversation with John N. Mitchell, a former attorney general under Nixon who was Nixon’s 1972 campaign chief.

He and Mitchell were uncomfortable with the idea, Magruder told PBS, so Mitchell suggested that he immediately call H.R. Haldeman, the White House chief of staff, to ask him whether to go ahead with the plan. He made the telephone call in Mitchell’s presence, he said.

“Yes, the president wants it done,” Haldeman said over the phone, according to Magruder. Haldeman than asked to speak to Mitchell. While they were speaking, Magruder said he could hear the president come on the line.

“I could hear the president talking to him,” he said, “and it was simply, you know, ‘John, we need to get that information on Larry O’Brien, the only way we can do that is through Liddy’s plan, and you need to do that.’ Nixon was saying we want Liddy to break into the Watergate.”

Magruder said he recognized Nixon’s unmistakable voice.

The Richard Nixon Library and Birthplace Foundation in California said that Magruder’s allegation contradicted Magruder’s own assertion in his memoir, “An American Life: One Man’s Road to Watergate” (1974). In that book he wrote, “I know nothing to indicate that Nixon was aware in advance of the plan to break into the Democratic headquarters.”

The Nixon library said the White House Daily Diary had recorded no calls to Key Biscayne on March 30. Nor did White House tapes corroborate such a call, the library said.

Fred LaRue, a Nixon aide who was convicted for his part in covering up Watergate, also questioned Magruder’s assertion. He said he had been at the meeting in Key Biscayne, charged with screening all telephone calls. He denied there was a call and said Magruder was “a congenital liar.”

But Carl Bernstein, who led the way in Watergate coverage at The Washington Post with his colleague Bob Woodward, said in an interview with CNN in 2003 that Magruder’s assertion had credibility.

“I find it compelling,” Bernstein said. “I find it more than plausible.”

Jeb Stuart Magruder was born Nov. 5, 1934, in Staten Island, New York. His father, who owned a print shop and was a Civil War buff, named him after J.E.B. Stuart, the Confederate general.

Magruder majored in political science at Williams College in Massachusetts, interrupting his studies after two years to serve in the Army in Korea. After returning to Williams, he studied ethics with the Rev. William Sloan Coffin, who was later chaplain at Yale. He excelled at swimming and tennis.

Interested in a career in sales, he spent one college summer promoting cough medicine. He also sold cosmetics to help pay for his studies. After graduating from Williams he worked for Crown-Zellerbach Corp. in San Francisco. He then moved to Kansas City, Missouri, where he drove a Jewel Tea truck delivering groceries. From there he went to Chicago, where he worked for Booz Allen & Hamilton and earned an MBA from the University of Chicago. In Los Angeles, he started two cosmetics companies.

Magruder had become a Republican in college and worked in Republican campaigns, including Donald Rumsfeld’s successful bid for the House of Representatives in Illinois in 1962 and Sen. Barry Goldwater’s losing presidential race in 1964. Magruder was a Southern California coordinator for Nixon’s 1968 presidential campaign.

He joined the Nixon White House in 1969 as a deputy to Herbert G. Klein, director of communications. He was later assigned to the president’s re-election campaign, where he assumed management duties. Nixon defeated Sen. George S. McGovern, the Democratic standard-bearer, in 49 of 50 states.

After serving as director of Nixon’s second inauguration, Magruder was assigned to the Commerce Department as director of policy planning.

Magruder’s marriages to Gail Barnes Nicholas and Patti Newton Filipski ended in divorce. He is survived by his sons Whitney, Justin and Stuart; his daughter, Tracy Sennett; and nine grandchildren.

After earning his theological degree, Magruder was ordained a Presbyterian minister in 1984. He was a church pastor in San Mateo, California; Columbus, Ohio; and Lexington, Kentucky.

In Columbus, the mayor appointed him chairman of a commission on values and ethics. In an interview, Magruder said his reflecting on Watergate had changed his values for the better.

“If they haven’t changed,” he said, “then it has been a real waste of time, hasn’t it?”